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E-GEOD-24538 - Ab initio identification of transcription start sites (TSSs) in the Rhesus macaque genome by histone modification and RNA-Seq

Status
Released on 18 October 2010, last updated on 6 November 2012
Organism
Macaca mulatta
Samples (3)
Protocols (3)
Description
We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures in the macaque brain. We then integrated the two types of our newly generated data with genomic sequence features and extended a TSS prediction algorithm to ab initio predict and verify 16,833 of previously electronically annotated transcription start sites at 500 bp resolution and predicted ~10,000 new TSSs. We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)’s ability to mark transcription start sites (TSSs) and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures. By integrating the ChIP-seq, RNA-seq and small RNA-seq data (previously uploaded to GEO as GSM450615 by our collaborator) with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified previously electronically annotated TSSs at a high resolution, and predicted some novel TSSs.
Experiment types
ChIP-seq, RNA-seq of coding RNA 
Contacts
Dali Han <handali294@gmail.com>, Bin Xie, Haiyang Hu, Jing Li, Jing-Dong J Han, Nan Qiao, Philipp Khaitovich, Yi Liu, Yixing Han, Yuan Gao, Zheng Yan
Citation
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Liu Y, Han D, Han Y, Yan Z, Xie B, Li J, Qiao N, Hu H, Khaitovich P, Gao Y, Han JD. , PMID:20952408
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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